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Eliminating C & E --- because we need a be form after malaria
B --- redundant construction
In A & D -- Picking A (have been rather than having been) as this condition is not true anymore. Also, believed to is idiomatic than believed as.
Although A is not the ideal construction, it is the best among the available choices.
Hope this helps. I am terrible at explaining :)
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"being" and "having been" are incorrect and A is the only one that is remotely correct.

I'm not a big fan of Princeton Review Verbal questions though.
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A is correct here. The sentence is in passive voice construction, that's why to have been is correct.
And if u are considering C as an option, then Please not in C verb is missing and hence there is no SV pair in the 1st clause.
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Original sentence is correct. ‘To have been’ is in sync with ‘has caused’
B. believed as being is awkward
C. Although Malaria doesn’t have a main verb. So, comma after malaria is wrong
D. believed as having been is incorrect
E. Contains same errors as B and C
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First Split :

C : Although Malaria...................The recent excavation............ : ( removing the middle modifier, the stem reduces to ) : Does it make any sense ? = Eliminated

E : Although Malaria...................The recent excavation............ : ( removing the middle modifier, the stem reduces to ) : Does it make any sense ? = Eliminated

2nd Split :

A : ..............Malaria was believed to have been......................... introduced to X

B : ..............Malaria was believed as having been...................... inroduced to X

D : ..............Malaria was believed as having been.......................introduced to X

Believed To ........... SCORES OEVR..............Believed AS ; thus B / D Eliminated

leading to A = my take
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OPEN DISCUSSION OF THIS QUESTION IS HERE: although-malaria-was-once-universally-believed-to-have-been-introduced-225612.html

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